ClinVar Miner

Submissions for variant NM_004958.4(MTOR):c.3117+34G>A

gnomAD frequency: 0.00001  dbSNP: rs545304092
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Brain Malformations Variant Curation Expert Panel RCV001837022 SCV001949978 benign Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes 2022-02-11 reviewed by expert panel curation This NM_004958.4(MTOR): c.3117+34G>A (p.=) variant is a synonymous (silent) variant that occurs at a nucleotide that is not conserved according to a PhyloP <0.1 (BP7). The results from in silico splicing predictors MaxEntScan, spliceAI and varSEAK support that this variant does not affect splicing (BP4). The highest population minor allele frequency in gnomAD v2.1.1 is 0.004847 in the South Asian population, which is higher than the ClinGen BMEP threshold ([>=0.00185]) for BA1, and therefore meets this criterion (BA1). This variant was identified the homozygous state in >3 individuals within control databases (BS2). In summary, this variant meets the criteria to be classified as Benign for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: BA1, BP4, BP7, BS2 ; -14 points (VCEP specifications version 1; Approved: 1/31/2021)
GeneDx RCV001690116 SCV001910488 benign not provided 2020-04-13 criteria provided, single submitter clinical testing

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